On 4/21/20 2:08 AM, Rolly Ng wrote:
Dear Gromacs user and Dr. lemkul,
I think my previous email is too large to send on the list. Could you
please kindly look at the link for the plots?
https://www.researchgate.net/post/GROMACS_2020_pull_code_produces_strange_Potential_Mean_Force_PMF_result
I don't see how the PMF could possibly arise from your data. The
reaction coordinate extends from 2 - 6 nm, but your PMF plot goes from 0
- 10 nm.
I tried to applied the umbrella tutorial to my protein-protein system,
and I am using GROMACS 2020
http://www.mdtutorials.com/gmx/umbrella/index.html
I have very dense windows to 0.1nm as shown on the attached histogram,
but as I look at the PMF curve, it is strange and incomplete?
I hope you're not directly applying the tutorial; there are some aspects
of it (use of restraints, the window spacing, and the restraint only
along z) that are not applicable to general protein-protein complexes.
Could you please help me to check what has gone wrong?
What was your gmx wham command? I really don't understand how it could
have even produced that PMF given the data you have in the histograms.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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